By Agence France-Presse
Andrew Wheeler has been acting head of the EPA since Scott Pruitt resigned in July amid a flurry of ethics scandals over his spending and conduct in office.
During an informal moment at a medal ceremony in the White House, Trump commended Wheeler's work and said he is "going to be made permanent" at the EPA.
Such appointments for cabinet positions still require Senate approval, which will likely not be a problem in the Republican-held chamber.
Wheeler, like Pruitt before him, has worked systematically to undo many of the environmental regulations put in place by Trump's Democratic predecessor Barack Obama.
Among these are the scrapping of anti-pollution rules for coal-fired power plants and the launch of a procedure to soften emissions standards for cars after 2025.
Such measures are facing challenges in the courts.